…reference material for story, setting and characterisation…
First and foremost, you have to set the plot up. Don't even think about characters, just about what's going to happen. From there, you think about setting. Where would this plot best fit? The real world? A contrasted one? Present, past, future? Then you start diving in and thinking about characters, personalities, backstory, etc.
As for reference material, I look to stuff I like. I'm a fan of medieval European history, so one of the things I referenced for a country in my (still being planned) setting was the Holy Roman Empire. What do you like? History, biology, biking? Taking something you enjoy doing or reading about and incorporating it is a great way to add something to the story.
…how to plan well (mindmaps and drafting doesn’t seem to help too much)…
Do what seems to work best for you. It could be a detailed outline of every plot point, a timeline of events that happen, little synopsis-like blurbs for chapters, or even something as simple as writing down the chapter titles and then spending a couple weeks just thinking about ideas in your spare time.
I've found writing an encyclopedia-like thing works well for me, coupled with the chapter title one.
how to avoid cliches while at the same time being able to use character archetypes in a good way
I've had a lot of fun reading TV Tropes, a Wikipedia-like site that covers many, many plots, characterization types, and cliches. Be warned that it can become quite engrossing.
…the Bible…
It can be quite complex, especially when dealing with the symbolism. There's stuff at the start that's brought up near the end, stuff that might be brought up later if you're reading this translation, or that. I'd recommending reading Psalms, Proverbs, one of the minor prophets (Haggai, Zephaniah, etc.), and Revelation to get a basic idea of some of the stuff at work. My preference is KJV.
Most importantly, though: write. Try and set aside some time each day to write. It could be little oneshots, or scenes from your big story. But whatever it is, just write something. The best way to become better at something is to practice doing it, after all.